Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_013553217.1 NITSA_RS01280 tryptophan synthase subunit alpha
Query= uniprot:H0BV16 (269 letters) >NCBI__GCF_000186245.1:WP_013553217.1 Length = 246 Score = 154 bits (390), Expect = 1e-42 Identities = 86/234 (36%), Positives = 136/234 (58%), Gaps = 10/234 (4%) Query: 17 KALIPYVTAGFPFADITPALMHGMVEAGADVIELGVPFSDPMADGPVIQKAGEKALSLGI 76 K L+ Y+T G+P T L + EAG D +ELG+PFSDP+ADGPVI+ A KAL G Sbjct: 2 KKLVAYITTGYPDKAFTVDLALALAEAGVDTLELGIPFSDPVADGPVIESANLKALQKGF 61 Query: 77 GMVQVLDHVREFRKRNNTTPVVLMGYANPVERYDQKHGEGAFVRDSAAAGVDGVLIVDYP 136 + + + R +T + MGY NP G F+ ++ A+GV+G +I D P Sbjct: 62 RIADLFEVSRSIAPAIDT---LWMGYFNPFYH----KGMETFIAEAKASGVNGFIIPDLP 114 Query: 137 PEECEAFAASLRAHGMDLIFLLAPTSTDERMAEVARVASGYVYYVSLKGVTGSGALDTAA 196 EE +A+ + G++LI +APT T ER+A +AR A ++Y V+ G+TGSG + Sbjct: 115 YEEAQAYKPMIEEAGLNLIDFIAPTDTPERIAMIARDAKKFLYLVAYAGITGSG--QSEE 172 Query: 197 VEQMLPRIRQHVTIPVGVGFGIRDAATAQAIGKVADAVVIGSRIIQLIEDQEHA 250 + +++ +IR+ PV VGFG+ + TA+ K D V++GS ++++ D++ + Sbjct: 173 LSEVIAQIRKQTQTPVYVGFGV-NPDTAKEKAKGVDGVIVGSAFVKILLDEDRS 225 Lambda K H 0.321 0.137 0.389 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 186 Number of extensions: 12 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 269 Length of database: 246 Length adjustment: 24 Effective length of query: 245 Effective length of database: 222 Effective search space: 54390 Effective search space used: 54390 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 bits)
Align candidate WP_013553217.1 NITSA_RS01280 (tryptophan synthase subunit alpha)
to HMM TIGR00262 (trpA: tryptophan synthase, alpha subunit (EC 4.2.1.20))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00262.hmm # target sequence database: /tmp/gapView.10556.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00262 [M=256] Accession: TIGR00262 Description: trpA: tryptophan synthase, alpha subunit Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-65 205.8 0.2 3e-65 205.6 0.2 1.0 1 lcl|NCBI__GCF_000186245.1:WP_013553217.1 NITSA_RS01280 tryptophan synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000186245.1:WP_013553217.1 NITSA_RS01280 tryptophan synthase subunit alpha # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 205.6 0.2 3e-65 3e-65 11 252 .. 3 237 .. 1 242 [. 0.90 Alignments for each domain: == domain 1 score: 205.6 bits; conditional E-value: 3e-65 TIGR00262 11 afvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkvekalellk 79 +v+++t+g+Pd + +++++ l++aG+d lElG+pfsDP+aDGp+i +a+l+Al++g+++++ +e+ + lcl|NCBI__GCF_000186245.1:WP_013553217.1 3 KLVAYITTGYPDKAFTVDLALALAEAGVDTLELGIPFSDPVADGPVIESANLKALQKGFRIADLFEVSR 71 69*************************************************************999998 PP TIGR00262 80 kvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhgvkqiflva 148 + +i + y+n+ ++kg+e+F+a+ak++gv+g +++DlP+eea+ + + ++ g++ i +a lcl|NCBI__GCF_000186245.1:WP_013553217.1 72 SIAP---AIDTLWMGYFNPFYHKGMETFIAEAKASGVNGFIIPDLPYEEAQAYKPMIEEAGLNLIDFIA 137 8865...5999********************************************************** PP TIGR00262 149 PtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGiskkeqvkelk 217 Pt +er+ ia+ ++ f Ylv+ aG+tg + +ee++e+i+++++ +++Pv vGFG+ ++ lcl|NCBI__GCF_000186245.1:WP_013553217.1 138 PTDTPERIAMIARDAKKFLYLVAYAGITGSGQ--SEELSEVIAQIRKQTQTPVYVGFGVNPDTAKEK-- 202 *****************************876..68899********************65544444.. PP TIGR00262 218 elgadgvivGsAlvkiieeklddeekaleeleefv 252 + g dgvivGsA+vki+ ++ ++ +e++ +++ lcl|NCBI__GCF_000186245.1:WP_013553217.1 203 AKGVDGVIVGSAFVKILLDEDRSLTERIEAVSQMA 237 4567************9766444444455555544 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (246 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.03 # Mc/sec: 1.74 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory